The very early stage of an R package wrapping the Ensembl REST api.
This package is very much a work in progress, and the behaviour may well change in the future. Even so, there is some stuff to play with already. You can install the package via devtools
devtools::install_github("dwinter/rensembl")Our development plan is to work on low-level functions that return simple R objects (lists or character vectors), then build some higher-level functions hat impliment common tasks or return richer R objects
Though we have only low level functions at present, some of them are quite helpful:
brca2_info <- lookup_symbol("BRCA2") brca2_info #> $source #> [1] "ensembl_havana" #> #> $object_type #> [1] "Gene" #> #> $logic_name #> [1] "ensembl_havana_gene" #> #> $species #> [1] "homo_sapiens" #> #> $description #> [1] "breast cancer 2, early onset [Source:HGNC Symbol;Acc:HGNC:1101]" #> #> $display_name #> [1] "BRCA2" #> #> $assembly_name #> [1] "GRCh38" #> #> $biotype #> [1] "protein_coding" #> #> $end #> [1] 32400266 #> #> $seq_region_name #> [1] "13" #> #> $db_type #> [1] "core" #> #> $strand #> [1] 1 #> #> $id #> [1] "ENSG00000139618" #> #> $start #> [1] 32315474snps <- overlap(gene_id=brca2_info$id, feature="variation") snps[[1]] #> $feature_type #> [1] "variation" #> #> $alt_alleles #> $alt_alleles[[1]] #> [1] "T" #> #> $alt_alleles[[2]] #> [1] "G" #> #> #> $assembly_name #> [1] "GRCh38" #> #> $end #> [1] 32315494 #> #> $seq_region_name #> [1] "13" #> #> $consequence_type #> [1] "5_prime_UTR_variant" #> #> $strand #> [1] 1 #> #> $id #> [1] "rs546292946" #> #> $start #> [1] 32315494We can extract some information for each case too:
table(sapply(snps, "[[", "consequence_type")) #> #> 3_prime_UTR_variant 5_prime_UTR_variant #> 66 20 #> coding_sequence_variant frameshift_variant #> 932 1041 #> inframe_deletion inframe_insertion #> 38 3 #> intron_variant missense_variant #> 2721 1369 #> non_coding_transcript_exon_variant protein_altering_variant #> 65 1 #> splice_acceptor_variant splice_donor_variant #> 60 66 #> splice_region_variant start_lost #> 118 3 #> stop_gained synonymous_variant #> 346 189